# Illumina Connected Analytics

## Illumina Connected Analytics

- [Introduction](https://help.ica.illumina.com/readme.md)
- [About the Platform](https://help.ica.illumina.com/get-started/gs-abouttheplatform.md)
- [Get Started](https://help.ica.illumina.com/get-started/gs-getstarted.md)
- [Projects](https://help.ica.illumina.com/home/h-projects.md)
- [Bundles](https://help.ica.illumina.com/home/h-bundles.md)
- [Event Log](https://help.ica.illumina.com/home/h-eventlog.md)
- [Metadata Models](https://help.ica.illumina.com/home/h-metadatamodels.md)
- [Docker Repository](https://help.ica.illumina.com/home/h-dockerrepository.md)
- [Tool Repository](https://help.ica.illumina.com/home/h-toolrepository.md)
- [Storage](https://help.ica.illumina.com/home/h-storage.md)
- [Connect AWS S3 Bucket](https://help.ica.illumina.com/home/h-storage/s-awss3.md)
- [IAM User Method](https://help.ica.illumina.com/home/h-storage/s-awss3/iam-user-method.md)
- [IAM Role Method](https://help.ica.illumina.com/home/h-storage/s-awss3/iam-role-method.md)
- [SSE-KMS Encryption](https://help.ica.illumina.com/home/h-storage/s-awss3/s-sse-kms.md)
- [Troubleshooting AWS-S3 Connectivity](https://help.ica.illumina.com/home/h-storage/s-awss3/troubleshooting-aws-s3-connectivity.md)
- [Data](https://help.ica.illumina.com/project/p-data.md)
- [Non-Indexed Folders](https://help.ica.illumina.com/project/p-data/non-indexed-folders.md)
- [Data Integrity](https://help.ica.illumina.com/project/p-data/data-integrity.md)
- [Storage Cost Managment](https://help.ica.illumina.com/project/p-data/storage-cost-managment.md)
- [Data - Troubleshooting](https://help.ica.illumina.com/project/p-data/data-troubleshooting.md)
- [Samples](https://help.ica.illumina.com/project/p-samples.md)
- [Activity](https://help.ica.illumina.com/project/p-activity.md)
- [Flow](https://help.ica.illumina.com/project/p-flow.md)
- [Reference Data](https://help.ica.illumina.com/project/p-flow/f-referencedata.md)
- [Pipelines](https://help.ica.illumina.com/project/p-flow/f-pipelines.md)
- [Nextflow](https://help.ica.illumina.com/project/p-flow/f-pipelines/pi-nextflow.md)
- [CWL](https://help.ica.illumina.com/project/p-flow/f-pipelines/pi-cwl.md)
- [XML Input Form](https://help.ica.illumina.com/project/p-flow/f-pipelines/pi-inputform.md)
- [JSON-Based input forms](https://help.ica.illumina.com/project/p-flow/f-pipelines/json-based-input-forms.md)
- [inputForm.json](https://help.ica.illumina.com/project/p-flow/f-pipelines/json-based-input-forms/inputform-json.md)
- [JSON Schema](https://help.ica.illumina.com/project/p-flow/f-pipelines/json-based-input-forms/inputform-json/inputform.json-syntax.md)
- [onRender.js](https://help.ica.illumina.com/project/p-flow/f-pipelines/json-based-input-forms/onrender.js.md)
- [onSubmit.js](https://help.ica.illumina.com/project/p-flow/f-pipelines/json-based-input-forms/onsubmit.js.md)
- [onFinished.js](https://help.ica.illumina.com/project/p-flow/f-pipelines/json-based-input-forms/onfinished.js.md)
- [JSON Scatter Gather Pipeline](https://help.ica.illumina.com/project/p-flow/f-pipelines/json-based-input-forms/json-scatter-gather-pipeline.md)
- [Git-Sourced Pipelines](https://help.ica.illumina.com/project/p-flow/f-pipelines/git-sourced-pipelines-experimental.md)
- [Basic Git-Sourced Pipeline Example](https://help.ica.illumina.com/project/p-flow/f-pipelines/git-sourced-pipelines-experimental/basic-git-sourced-pipeline-example.md)
- [Tips and Tricks](https://help.ica.illumina.com/project/p-flow/f-pipelines/pi-tips.md)
- [Analyses](https://help.ica.illumina.com/project/p-flow/f-analyses.md)
- [Base](https://help.ica.illumina.com/project/p-base.md)
- [Tables](https://help.ica.illumina.com/project/p-base/base-tables.md)
- [Data Catalogue](https://help.ica.illumina.com/project/p-base/base-tables/datacatalogue.md)
- [Query](https://help.ica.illumina.com/project/p-base/base-query.md)
- [Schedule](https://help.ica.illumina.com/project/p-base/base-schedule.md)
- [Snowflake](https://help.ica.illumina.com/project/p-base/base-snowflake.md)
- [Bench](https://help.ica.illumina.com/project/p-bench.md)
- [Workspaces](https://help.ica.illumina.com/project/p-bench/bench-workspaces.md)
- [Bench Clusters](https://help.ica.illumina.com/project/p-bench/bench-workspaces/bench-clusters.md)
- [Sun Grid Engine (SGE) on ICA Bench](https://help.ica.illumina.com/project/p-bench/bench-workspaces/sun-grid-engine-sge-on-ica-bench.md)
- [Spark on ICA Bench](https://help.ica.illumina.com/project/p-bench/bench-workspaces/spark-on-ica-bench.md): Running a Spark application in a Bench Spark Cluster
- [JupyterLab](https://help.ica.illumina.com/project/p-bench/bench-jupyterlab.md)
- [Bring Your Own Bench Image](https://help.ica.illumina.com/project/p-bench/bring-your-own-bench-image.md)
- [Bench Command Line Interface](https://help.ica.illumina.com/project/p-bench/bench-command-line-interface.md)
- [Pipeline Development in Bench (Experimental)](https://help.ica.illumina.com/project/p-bench/pipeline-development-in-bench-experimental.md)
- [Creating a Pipeline from Scratch](https://help.ica.illumina.com/project/p-bench/pipeline-development-in-bench-experimental/creating-a-pipeline-from-scratch.md)
- [nf-core Pipelines](https://help.ica.illumina.com/project/p-bench/pipeline-development-in-bench-experimental/nf-core-pipelines.md)
- [Updating an Existing Flow Pipeline](https://help.ica.illumina.com/project/p-bench/pipeline-development-in-bench-experimental/updating-an-existing-flow-pipeline.md)
- [Containers in Bench](https://help.ica.illumina.com/project/p-bench/containers-in-bench.md)
- [FUSE Driver](https://help.ica.illumina.com/project/p-bench/bench-fusedriver.md)
- [Run DRAGEN in Bench - Interactive](https://help.ica.illumina.com/project/p-bench/run-dragen-in-bench-interactive.md)
- [Cohorts](https://help.ica.illumina.com/project/p-cohorts.md)
- [Create a Cohort](https://help.ica.illumina.com/project/p-cohorts/cohorts-create.md)
- [Import New Samples](https://help.ica.illumina.com/project/p-cohorts/cohorts-import.md)
- [Prepare Metadata Sheets](https://help.ica.illumina.com/project/p-cohorts/cohorts-metadata.md)
- [Precomputed GWAS and PheWAS](https://help.ica.illumina.com/project/p-cohorts/cohorts-gwas-phewas.md)
- [Cohort Analysis](https://help.ica.illumina.com/project/p-cohorts/cohorts-analysis.md)
- [Compare Cohorts](https://help.ica.illumina.com/project/p-cohorts/cohorts-comparison.md)
- [Cohorts Data in ICA Base](https://help.ica.illumina.com/project/p-cohorts/cohorts-base.md)
- [Oncology Walk-through](https://help.ica.illumina.com/project/p-cohorts/cohorts-walkthrough-cancer.md)
- [Rare Genetic Disorders Walk-through](https://help.ica.illumina.com/project/p-cohorts/cohorts-walkthrough-raredisease.md)
- [Public Data Sets](https://help.ica.illumina.com/project/p-cohorts/cohorts-publicdata.md)
- [Details](https://help.ica.illumina.com/project/p-details.md)
- [Team](https://help.ica.illumina.com/project/p-team.md)
- [Connectivity](https://help.ica.illumina.com/project/p-connectivity.md)
- [Service Connector](https://help.ica.illumina.com/project/p-connectivity/service-connector.md)
- [Service Connector Troubleshooting](https://help.ica.illumina.com/project/p-connectivity/service-connector/service-connector-troubleshooting.md)
- [Project Connector](https://help.ica.illumina.com/project/p-connectivity/project-connector.md)
- [Notifications](https://help.ica.illumina.com/project/p-notifications.md)
- [Installation](https://help.ica.illumina.com/command-line-interface/cli-installation.md)
- [Authentication](https://help.ica.illumina.com/command-line-interface/cli-authentication.md)
- [Data Transfer](https://help.ica.illumina.com/command-line-interface/cli-datatransfer.md)
- [Config Settings](https://help.ica.illumina.com/command-line-interface/cli-configsettings.md)
- [Output Format](https://help.ica.illumina.com/command-line-interface/cli-outputformat.md)
- [Command Index](https://help.ica.illumina.com/command-line-interface/cli-indexcommands.md)
- [Releases](https://help.ica.illumina.com/command-line-interface/cli-releasehistory.md)
- [Cloud Analysis Auto-launch](https://help.ica.illumina.com/sequencer-integration/analysis_autolaunch.md)
- [Nextflow Pipeline](https://help.ica.illumina.com/tutorials/nextflow.md)
- [Nextflow DRAGEN Pipeline](https://help.ica.illumina.com/tutorials/nextflow/nextflow-dragen-pipeline.md)
- [Nextflow: Scatter-gather Method](https://help.ica.illumina.com/tutorials/nextflow/scatter-gather-nextflow.md)
- [Nextflow: Pipeline Lift](https://help.ica.illumina.com/tutorials/nextflow/nextflow_pipeline_liftovers.md)
- [Nextflow CLI](https://help.ica.illumina.com/tutorials/nextflow/nextflow-cli-tutorial.md)
- [CWL CLI Pipeline Execution](https://help.ica.illumina.com/tutorials/cli-cwl.md)
- [CWL Graphical Pipeline](https://help.ica.illumina.com/tutorials/cli-cwl/cwl-graphical-pipeline.md)
- [CWL DRAGEN Pipeline](https://help.ica.illumina.com/tutorials/cli-cwl/cwl-dragen-pipeline.md)
- [CWL: Scatter-gather Method](https://help.ica.illumina.com/tutorials/cli-cwl/scatter-gather.md)
- [Base Basics](https://help.ica.illumina.com/tutorials/base_basics.md)
- [Base: SnowSQL](https://help.ica.illumina.com/tutorials/base_basics/base_snowsql.md)
- [Base: Access Tables via Python](https://help.ica.illumina.com/tutorials/base_basics/dashboard.md)
- [Bench ICA Python Library](https://help.ica.illumina.com/tutorials/bench-ica-python-library.md)
- [API Beginner Guide](https://help.ica.illumina.com/tutorials/api-introduction.md)
- [Launching a DRAGEN Pipeline](https://help.ica.illumina.com/tutorials/launching-a-dragen-pipeline.md)
- [End-to-End User Flow: DRAGEN Analysis](https://help.ica.illumina.com/tutorials/end-to-end-1.md)
- [Data Transfer Options](https://help.ica.illumina.com/tutorials/datatransfer.md)
- [Pipeline Chaining on AWS](https://help.ica.illumina.com/tutorials/pipeline_chaining_aws.md)
- [Software Release Notes](https://help.ica.illumina.com/reference/software-release-notes.md)
- [2026](https://help.ica.illumina.com/reference/software-release-notes/2026.md)
- [2025](https://help.ica.illumina.com/reference/software-release-notes/2025.md)
- [2024](https://help.ica.illumina.com/reference/software-release-notes/2024.md)
- [2023](https://help.ica.illumina.com/reference/software-release-notes/2023.md)
- [2022](https://help.ica.illumina.com/reference/software-release-notes/2022.md)
- [2021](https://help.ica.illumina.com/reference/software-release-notes/2021.md)
- [Known Issues](https://help.ica.illumina.com/reference/r-knownissues.md)
- [API](https://help.ica.illumina.com/reference/r-api.md)
- [Pricing](https://help.ica.illumina.com/reference/r-pricing.md)
- [Security and Compliance](https://help.ica.illumina.com/reference/r-securityandcompliance.md)
- [Network Settings](https://help.ica.illumina.com/reference/r-networksettings.md)
- [ICA Terminology](https://help.ica.illumina.com/reference/r-terms.md)
- [External Resources](https://help.ica.illumina.com/reference/r-resources.md)
- [Data Formats](https://help.ica.illumina.com/reference/r-dataformats.md)
- [FAQ](https://help.ica.illumina.com/reference/r-faq.md)


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